Two typical areas, including once commercial and residential quarters of Nanjing, China, were studied by investigating soil properties especially heavy metals of soils in various cultural layers formed in different Chinese Dynasties. The age of the soil profiles was dated by both archaeological and 14C chronological methods. The results showed that urban soils in the old commercial/workshop quarter of Nanjing were generally contaminated by heavy metals Cu, Zn, Pb, but their concentration levels varied significantly among the cultural layers formed in different dynasties. The substantial increase of heavy metals appeared in three historical periods, i.e., South Dynasty (222-589 AD), the earlier Ming (1368-1644 AD) and the late Qing (1644-1912 AD) in one area. The tremendous input and storage of heavy metals in soils was explained by the primitive smelting and the strengthened metal processing activities, which might be due to the requirement of weapon making or other industries, in the changing social conditions of the corresponding periods. Soils in the once noble political, cultural centers did not show significant increase of heavy metals. The difference in the distribution pattern of heavy metals revealed the contrasting history of the site uses. The change of contaminant level in soils is believed to be a reflection of various human activities in the city during the past 20 centuries.